New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library (...) !
BioRuby project
20 months
30
12
83909
8534
Parser of scientific names (...) !
Dmitry Mozzherin
5 months
18
5
43673
3929
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
2 weeks
5
1
38653
4415
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
8 months
14
11
35020
2845
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
3 months
17
5
31652
4470
0
0
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
4 months
2
...
27291
3275
0
9
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
10 months
13
1
22628
2155
0
0
Http requests to entrez e-utilities (...)
Jared Ning
3 years
4
...
21804
1641
A Ruby api for interacting with biomart services (...) !
Darren Oakley
3 years
17
4
21621
1266
Gadgets for bioinformatics (...)
Shintaro Katayama
20 months
...
21457
2723
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
10 months
...
21054
2935
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
7 weeks
30
19
18787
1923
34
126
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
17339
1254
0
0
Create pretty svg-format images of features, gene models (...)
Dan MacLean
13 months
9
5
16214
3331
0
0
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
30
16170
1658
Interfaces with biomodel search engine (...) !
Niall Beard
2 years
...
14779
1148
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
13979
1486
0
0
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
13872
1672
0
0
A simple obo file handler (...) !
mjy
3 years
4
...
12946
859
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
2 months
12
...
12936
2409
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
10210
877
0
0
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
8 months
7
5
9944
913
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
8 months
8
20
9715
1148
0
0
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
3 weeks
10
2
8808
2067
0
23
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
1
1
8642
615
0
0
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
23 months
1
...
8630
765
0
0
A nexus file format (phylogenetic inference) parser in (...) !
mjy
3 years
1
...
8324
487
Low memory sequence emitters (...)
Pjotr Prins
8 months
8
1
8184
748
0
0
Data mining algorithms for jRuby (...)
arrigonialberto86
16 months
14
3
8181
1384
0
0
Build genome output files (...)
Michael Barton
17 months
5
...
7884
529
0
0
Ruby support for the baclava file format (...) !
Robert Haines
11 months
1
...
7822
1850
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
6 months
1
...
7611
756
0
0
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
7589
497
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
7503
477
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
7211
622
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
2
7078
503
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
19 months
8
...
7038
520
0
0
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
10 months
...
6932
2170
0
0
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
2 years
3
...
6893
519
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
6890
636
0
0
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
20 months
5
...
6863
748
0
0
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
6818
421
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
6490
390
0
0
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
6311
406
0
0
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
29
14
6066
392
0
0
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
5792
379
0
0
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
5243
538
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
5101
388
0
0
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
9
...
5000
281
0
0
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
4889
381
0
0
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
3 months
2
...
4780
2062
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
18 months
11
2
4715
902
0
0
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
4686
368
0
0
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
30
5
4680
238
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
21 months
2
1
4565
497
0
0
Ruby binding for samtools tabix (...)
throwern
16 months
3
...
4303
513
Taverna player is a rails plugin to run (...)
Robert Haines
3 months
4
3
3911
871
0
4
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
3874
251
0
0
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
3874
379
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
3836
248
0
0
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
3819
393
0
0
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
3797
385
0
0
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
3786
363
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3601
280
0
3
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
3555
279
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3322
255
0
0
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
3151
259
0
0
Parser to work with file formats used in (...)
Ben J Woodcroft
3 weeks
...
3114
1050
0
8
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3090
252
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
16 months
...
3084
522
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
24 months
...
3012
367
Fast multi-threaded vcf parser (...)
Pjotr Prins
5 weeks
15
6
3001
1230
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
20 months
...
2895
371
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
17 months
1
...
2890
389
0
0
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2761
256
0
0
A protparam compatible utility for BioRuby (...)
hryk
2 years
1
...
2703
255
0
0
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
2602
252
0
0
Publish scientific results to the semantic web (...) !
Will Strinz
7 months
3
16
2292
352
0
0
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
3 months
...
2097
972
0
0
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2017
126
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
1998
131
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
1997
132
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
10 months
1
...
1931
515
0
0
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
4 years
1
...
1926
125
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
11 months
6
...
1854
173
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1740
125
0
0
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1728
120
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1709
133
0
0
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1702
136
0
0
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1678
120
0
0
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1670
131
0
0
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1657
136
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1632
129
0
0
Gggenome Ruby client (...)
Mitsuteru Nakao
17 months
1
...
1626
251
0
0
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1612
128
0
0
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1599
129
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1583
124
0
0
A general purpose framework for scripted handling of (...) development/stable
mjy
22 months
1
...
1560
150
Ruby ensembl rest api (...)
Alberto Donizetti
16 months
3
1
1541
250
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1488
136
0
0
Generalized linear models for statsample (...)
Ankur Goel
16 months
...
1487
248
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
3 weeks
1
1412
718
0
9
Build graph with jRuby (...)
Matteo Picciolini
2 years
...
1396
134
Biostars data-mining and statistical analysis (...)
Joachim Baran
9 months
1
...
1393
386
0
0
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
1
...
1390
132
0
0
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
...
1388
93
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
12 months
...
1229
253
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
12 months
...
1211
264
0
0
Bio-repeatmasker (...)
Andrei Rozanski
12 months
1197
258
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1139
132
0
0
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
2 months
...
1089
709
A parser for cigar format alignments (...)
Ben J Woodcroft
11 months
4
...
1055
269
0
0
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
5 years
4
...
1028
355
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
19 months
2
...
924
128
0
0
Web server for bio-samtools (...)
homonecloco
8 months
...
909
269
0
0
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
18 months
...
863
132
0
0
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
3 months
...
696
283
Mine publications for gene names (...)
Pjotr Prins
11 months
...
534
139
0
0
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
30
1
521
183
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
10 months
2
...
430
113
0
0
(...) pre
pre
385
19
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
6 months
...
380
145
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
6 weeks
1
...
357
357
0
11
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
4 months
...
303
154
Tools to work with fasta files, indexed with (...)
homonecloco
3 months
...
296
162
0
0
Tools to manipulate blat files from the command (...)
homonecloco
4 months
...
283
143
0
0
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
272
97
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
11 weeks
...
235
235
0
16
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
11 weeks
...
234
234
0
10
(...) pre
pre
127
28
!
Rocker (...) new
Luis (Coto) Orellana, Luis M. Rodriguez-R
1 week
114
114
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-02-01
**) number of commits on GitHub (last 7 days & last 90 days)